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Sequence 1:
>gi|6321538|ref|NP_011615.1| Pcp1p [Saccharomyces cerevisiae S288c]
MSGVSSVMLGLRPATRIFFRSNISVSPSRTFVSYIGRSQSTSILKNAPNLEDNVTNLQKIIPKRFFSQTSILKSRWKPIFNEETTNRYVRLNRFQQYQQQRSGGNPLGSMTILGLSLMAGIYFGSPYLFEHVPPFTYFKTHPKNLVYALLGINVAVFGLWQLPKCWRFLQKYMLLQKDYVTSKISIIGSAFSHQEFWHLGMNMLALWSFGTSLATMLGASNFFSLYMNSAIAGSLFSLWYPKLARLAIVGPSLGASGALFGVLGCFSYLFPHAKILLFVFPVPGGAWVAFLASVAWNAAGCALRWGSFDYAAHLGGSMMGVLYGWYISKAVEKQRQRRLQAAGRWF
Sequence 2:
>sp|P48740|MASP1_HUMAN Mannan-binding lectin serine protease 1 OS=Homo sapiens GN=MASP1 PE=1 SV=3
MRWLLLYYALCFSLSKASAHTVELNNMFGQIQSPGYPDSYPSDSEVTWNITVPDGFRIKLYFMHFNLESSYLCEYDYVKVETEDQVLATFCGRETTDTEQTPGQEVVLSPGSFMSITFRSDFSNEERFTGFDAHYMAVDVDECKEREDEELSCDHYCHNYIGGYYCSCRFGYILHTDNRTCRVECSDNLFTQRTGVITSPDFPNPYPKSSECLYTIELEEGFMVNLQFEDIFDIEDHPEVPCPYDYIKIKVGPKVLGPFCGEKAPEPISTQSHSVLILFHSDNSGENRGWRLSYRAAGNECPELQPPVHGKIEPSQAKYFFKDQVLVSCDTGYKVLKDNVEMDTFQIECLKDGTWSNKIPTCKIVDCRAPGELEHGLITFSTRNNLTTYKSEIKYSCQEPYYKMLNNNTGIYTCSAQGVWMNKVLGRSLPTCLPVCGLPKFSRKLMARIFNGRPAQKGTTPWIAMLSHLNGQPFCGGSLLGSSWIVTAAHCLHQSLDPEDPTLRDSDLLSPSDFKIILGKHWRLRSDENEQHLGVKHTTLHPQYDPNTFENDVALVELLESPVLNAFVMPICLPEGPQQEGAMVIVSGWGKQFLQRFPETLMEIEIPIVDHSTCQKAYAPLKKKVTRDMICAGEKEGGKDACAGDSGGPMVTLNRERGQWYLVGTVSWGDDCGKKDRYGVYSYIHHNKDWIQRVTGVRN
Theory:
• The method used to analyze the similarities and differences at the level of individual bases or amino acids with the aim of inferring structural, functional and evolutionary relationships among the sequences are called sequence alignment.
• A sequence alignment is a scheme of writing one sequence above of another where the residues in one position are deemed to have a common evolutionary origin. If the same letter occurs in both sequences then this position has been conserved in evolution. If the letters differ it is assumed that the two derive from an ancestral letter (which could be one of the two or neither). Homologous sequences may have different lengths, because of insertions or deletions in either sequence.
• Thus, a letter or a stretch of letters may be paired up with dashes in the other sequence to signify such insertions or deletions. Since an insertion in one sequence can always be seen as a deletion in the other one frequently uses the term "indel".
• An alignment that searches for segment of the two sequences that match well. There is no attempt to force entire sequence into alignment, and just those parts that appear to have good similarity are aligned.
• Local alignment is performed by Smith-Waterman algorithm.
Procedure:
• Respective protein sequences of human (NP_011615.1) and yeast (P48740) in Fasta format were retrieved from NCBI (ncbi.nlm.nih.gov) and ExPASy proteomic server (http://expasy) respectively.
• Log in to http://ebi.ac.uk/Tools/emboss/align/
• Paste the respective sequences in the given input boxes.
• Keep the method in Water (local) tool and remaining option buttons in default.
• Click run.
• Results were displayed as soon as the given job completed.